Novichok Nerve Agents as Inhibitors of Acetylcholinesterase-In Silico Study of Their Non-Covalent Binding Affinity

In silico studies were performed to assess the binding affinity of selected organophosphorus compounds toward the acetylcholinesterase enzyme (AChE). Quantum mechanical calculations, molecular docking, and molecular dynamics (MD) with molecular mechanics Generalized-Born surface area (MM/GBSA) were applied to assess quantitatively differences between the binding energies of acetylcholine (ACh; the natural agonist of AChE) and neurotoxic, synthetic correlatives (so-called "Novichoks", and selected compounds from the G- and V-series). Several additional quantitative descriptors like root-mean-square fluctuation (RMSF) and the solvent accessible surface area (SASA) were briefly discussed to give-to the best of our knowledge-the first quantitative in silico description of AChE-Novichok non-covalent binding process and thus facilitate the search for an efficient and effective treatment for Novichok intoxication and in a broader sense-intoxication with other warfare nerve agents as well.

Self-Restructuring of Polyhydromethylsiloxanes by the Hydride Transfer Process: A New Approach to the Cross-Linking of Polysiloxanes and to the Fabrication of Thin Polysiloxane Coatings

The branching and cross-linking of siloxane polymers are important processes in silicone technology. A new type of such a process has been developed, which is a self-restructuring of linear polyhydromethylsiloxane (PHMS). This process involves the reorganization of the PHMS to form a highly branched siloxane polymer or finally a cross-linked siloxane network. It occurs through the transfer of a hydride ion between silicon atoms catalyzed by tris(pentafluoromethyl)borane. Its advantage over existing branching and cross-linking reactions is that it runs at room temperature without a low-molecular-weight cross-linker in the absence of water, silanol groups, or other protic compounds and it does not use metal catalysts. The study of this process was carried out in toluene solution. Its course was followed by ¹H NMR, ²⁹Si NMR and FTIR, SEC, and gas chromatography. A general mechanism of this new self-restructuring process supported by quantum calculations is proposed. It has been shown that a linear PHMS self-restructured to a highly branched polymer can serve as a pure methylsiloxane film precursor.

Correction: Mikołajczyk et al. Nucleophilic Substitution at Heteroatoms-Identity Substitution Reactions at Phosphorus and Sulfur Centers: Do They Proceed in a Concerted (SN2) or Stepwise (A-E) Way? Molecules 2022, 27, 599

(1) The authors would like to correct mistakes in the title paper [...].

Reactions of Zirconium (IV) n-Propoxide with SiH-Functional Polysiloxanes as a Route to Siloxane-Zirconium Hybrid Materials with Enhanced Refractive Index

The reaction of poly(hydromethylsiloxane-co-methylphenylsiloxane) with zirconium (IV) n-propoxide in dry toluene leads to extensive scission of the siloxane chain and conversion of Si-H groups. These processes produce oligomeric siloxanes and organosilanes containing moisture sensitive propoxy and siloxy-zirconate groups. The obtained post-reaction solution of zirconium containing heterosiloxane oligomers is stable under anhydrous conditions for several weeks. However, its exposure to moisture initiates the hydrolytic condensation of the reactive groups leading to cross-linking and the formation of a siloxane-zirconium composite. Spin coating of the siloxane-zirconium prepolymer followed by exposure to moisture produces thin films with excellent light transparency and increased refractive index. The final coatings are characterized by ellipsometry, UV-Vis, IR, and ²⁹ Si MAS NMR spectroscopies.

Effect of temperature on B(C6F5)3-catalysed reduction of germanium alkoxides by hydrosilanes - a new route to germanium nanoparticles

Reduction of Ge(OBu)4 with PhMe2SiH catalyzed by B(C6F5)3 at ambient temperature leads to GeH4. We discovered that a higher temperature (above 100 °C) completely changes the reaction course by producing germanium nanoparticles (Ge NPs) in high yield. This process provides a simple one-pot method for Ge NPs synthesis from readily available substrates under mild conditions.

Reasons for enhanced activity of doxorubicin on co-delivery with octa(3-aminopropyl)silsesquioxane

This paper presents results of spectroscopic (NMR, FTIR, fluorescence), Q-TOF mass spectrometry and Z-potential analyses of interactions between octa(3-aminopropyl)silsesquioxane hydrochloride (POSS-NH₂·HCl) and anticancer drug – doxorubicin hydrochloride. These studies aimed at explanation of the enhanced activity of doxorubicin on co-delivery with POSS-NH₂. The results point to the formation of active complexes via ionic interactions between the ammonium chloride groups of silsesquioxane and the drug, and not, as suggested earlier, via NH⋯N hydrogen bonding. It has also been shown that the main driving force for the formation of the complexes can be strengthened by π–π stacking and hydrogen bonds. The experimental results are supported by quantum mechanical calculations. This work has proven that co-delivery with POSS offers a potentially advantageous and simple approach for improved efficacy in chemotherapy, avoiding often complicated synthesis of conjugates, involving covalent bonding between drug, nanocarrier and targeting agents.

The interaction between polyhedral oligomeric silsesquioxane (POSS) and doxorubicin, leading to formation of active complexes involving POSS functional aminopropyl groups and anthracycline functional groups.

Nucleophilic Substitution at Tetracoordinate Sulfur. Kinetics and Mechanism of the Chloride-Chloride Exchange Reaction in Arenesulfonyl Chlorides: Counterintuitive Acceleration of Substitution at Sulfonyl Sulfur by ortho-Alkyl Groups and Its Origin

The chloride-chloride exchange reaction in arenesulfonyl chlorides was investigated experimentally and theoretically by density functional theory (DFT) calculations. The second order rate constants and activation parameters of this identity reaction were determined for 22 variously substituted arenesulfonyl chlorides using radio-labeled Et₄N³⁶Cl. The chloride exchange rates of 11 sulfonyl chlorides bearing para-and meta-substituents (σ constants from -0.66 to +0.43) in the aromatic ring followed the Hammett equation with a ρ-value of +2.02. The mono- and di-ortho-alkyl substituted sulfonyl chlorides exhibit an enhanced reactivity although both inductive and steric effects lower the reaction rate. The DFT calculations of their structures together with X-ray data showed that an increased reactivity is mainly due to a peculiar, rigid, strongly compressed and sterically congested structure. The DFT studies of the title reaction revealed that it proceeds via a single transition state according to the S_N2 mechanism. The analogous fluoride exchange reaction occurs according to the addition-elimination mechanism (A-E) and formation of a difluorosulfurandioxide intermediate. The reliability of the calculations performed was supported by the fact that the calculated relative rate constants and activation parameters correlate well with the experimental kinetic data.

Hydrolysis of trialkoxysilanes catalysed by the fluoride anion. Nucleophilic vs. basic catalysis

A DFT study showed competition between basic and nucleophilic catalysis of alkoxysilane hydrolysis by the fluoride ion.

C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons

Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson–Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a ‘new wobble’ pattern.

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon–anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3′-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.

Differentiation of diastereoisomers of protected 1,2-diaminoalkylphosphonic acids by EI mass spectrometry and density functional theory

Electron ionization mass spectrometry and density functional theory (DFT) calculations have been used to study the fragmentation of diastereoisomers of protected 1,2-diaminoalkylphosphonic acids. The loss of a diethoxyphosphoryl group and the elimination of diethyl phosphonate were found to be competitive fragmentation processes, which can be used to differentiate both stereoisomers. Selective deuterated analogs and product- and precursor-ion mass spectra allowed the elucidation of the fragmentation mechanisms. The structures of the transition states and product ions were optimized using the density functional theory (DFT), and free energy calculations confirmed the observed differences in the formation and relative intensities of specific fragment ions.

Terpolymers of N-vinylpyrrolidinone and 1-vinylimidazole as new supports for palladium nanocluster catalysts

Two terpolymers of styrene, divinylbenzene, and 1-vinylimidazole (S/DVB/VI) or N-vinylpyrrolidinone (S/DVB/NVP) were prepared by radical polymerization. Palladium nanoparticle catalyst has been “heterogenized” by anchoring to these polymers the [PdCl2(PhCN)2] complex via ligand exchange reaction. The formation of coordination bond between S/DVB/VI, S/DVB/NVP terpolymers and Pd2+ ions was studied using infrared and XPS. Immobilized palladium complex was reduced during hydrogenation reaction or by reaction with sodium borohydride. Characterization of polymer supports and palladium catalysts has involved the measurements of the structural parameters in the dry state by the nitrogen BET adsorption, X-ray photoelectron spectroscopy (XPS), AAS spectroscopy and time-of-flight secondary ion mass spectrometry (TOF-SIMS). Both the catalytic systems were found efficient in the hydrogenation of cinnamaldehyde. The stability and a good recycling efficiency of these catalysts make them useful for prolonged use. The factors influencing selectivity of supported catalysts were discussed. The results offer the possibility of using these terpolymers for the immobilization of metal complex catalysts for hydrogenation and other catalytic reactions.

Synthesis of p-(di-tert-butyl[(18)F]fluorosilyl)benzaldehyde ([(18)F]SiFA-A) with high specific activity by isotopic exchange: a convenient labeling synthon for the (18)F-labeling of N-amino-oxy derivatized peptides

The syntheses of different (18)F-labeled peptides using the highly effective labeling synthon p-(di- tert-butylfluorosilyl) benzaldehyde ([ (18)F]SiFA-A) for the development of (18)F-radiopharmaceuticals for oncological positron emission tomography (PET) is reported. The novel and mild labeling technique for the radiosynthesis of [ (18)F]SiFA-A, based on an unexpectedly efficient isotopic (19)F- (18)F exchange, yielded the (18)F-synthon [ (18)F]SiFA-A in almost quantitative yields in high specific activities between 225 and 680 GBq/micromol (6081-18 378 Ci/mmol) without applying HPLC purification. The [ (18)F]SiFA-A was finally used to label the N-terminal amino-oxy (N-AO) derivatized peptides AO-Tyr (3)-octreotate (AO-TATE), cyclo(fK(AO-N)RGD and N-AO-PEG 2-[D-Tyr-Gln-Trp-Ala-Val-betaAla-His-Thi-Nle-NH 2] (AO-BZH3, a bombesin derivative) in high radiochemical yields. Density functional theory (DFT) calculations confirmed high efficiency of the isotopic exchange, which is predicted to proceed via a pentacoordinate siliconate intermediate dissociating immediately to form the radiolabeled [ (18)F]SiFA-A.

A novel class of DNA analogs bearing 5'-C-phosphonothymidine units: synthesis and physicochemical and biochemical properties

S(C) and R(C) diastereomers of 5'-C-(O,O-diethyl)-phosphonylthymidine ((R)T and (S)T) were used for the synthesis of the dimers T(R)T and T(S)T, respectively. These dimers were incorporated at selected sites in oligonucleotide constructs. Melting temperature (Tm) experiments demonstrated that relative to the unmodified oligodeoxyribonucleotide, the presence of the (R)T moiety reduced the thermal stability of the duplexes by approximately 5.0 degrees C per modification, whereas their (S)T counterparts only slightly destabilized the duplex structure (deltaTm < or = 1 degree C/modification). The stability of the triple-helical complexes containing one, two, or three modified thymidines is slightly higher than that of the parent complex. Nuclease resistance studies performed with snake venom phosphodiesterase, calf spleen phosphodiesterase, and 3'-exonuclease from human plasma showed that cleavage of the oligonucleotides at the site of the modification was completely suppressed regardless of the stereochemistry of the 5'-C-chiral center. The influence of the (R)T and (S)T modification in the recognition sequence of HindIII, EcoRI, and HpaI restriction endonucleases was also investigated. Although the catalytic activity of HindIII was not affected by the presence of the 5'-C-ethoxyphosphonyl modification, the activities of the two remaining restriction enzymes were partially suppressed depending on the site of modification or the stereochemistry of the modification or both ((R)T vs. (S)T).

Hydrolysis of Fluorosilanes: A Theoretical Study

Hydrolysis and condensation of simple trifluorosilanes, HSiF3 and MeSiF3, was studied by quantum mechanical methods. Hydrolysis of fluorosilanes is highly endothermic. The Gibbs free energy of the first reaction step in the gas phase is 31.4 kJ/mol, which corresponds to an equilibrium constant of 10(-6). Hydrolysis of the subsequent fluorine atoms in trifluorosilanes is thermodynamically more unfavorable than the first step of substitution. No significant difference in thermodynamics of hydrolysis was found between HSiF3 and MeSiF3. The activation energy for hydrolysis by a water dimer is significantly lower than that for hydrolysis by a water monomer. The former reaction is also less unfavorable thermodynamically, due to a high binding energy of the HF-H2O complex formed as a product of hydrolysis. Self-consistent reaction field (SCRF) calculations show that hydrolysis of trifluorosilanes in aqueous medium has lower activation energy than in the gas phase. It is also thermodynamically less unfavorable, due to better solvation of the products. Homofunctional condensation of HSiF2OH is thermodynamically favored. The equilibrium mixture for hydrolysis/condensation of RSiF3 in water is predicted to contain ca. 2.3% disiloxane (HF2Si)2O, if 100-fold excess of water relative to silane is assumed. Further hydrolysis of (HF2Si)2O is negligible. The thermodynamics of fluorosilane hydrolysis contrasts with that of chlorosilanes, where both hydrolysis and condensation are strongly favorable. Moreover, in the case of trichlorosilanes each subsequent hydrolysis step is more facile, leading to the product of full hydrolysis, RSi(OH)3.